Contacts of the helix formed by residues 788 - 809 (chain A) in PDB entry 3LMG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 788 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786A ALA 3.8 1.9 + - - -
787A LEU* 1.3 71.5 - - - +
789A PRO* 1.3 64.4 - - - +
790A GLN* 3.0 4.3 - - - -
791A LEU* 3.5 18.5 - - - +
792A LEU* 2.7 37.0 + - - +
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Residues in contact with PRO 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A LEU 3.5 6.9 - - - +
788A GLY* 1.3 83.1 - - - +
790A GLN* 1.3 60.8 + - + +
792A LEU* 4.5 5.2 - - + -
793A LEU* 3.4 29.6 + - - +
953A PRO* 4.2 14.6 - - + +
954A PRO* 5.0 10.1 - - + -
957A LEU* 4.0 28.7 - - + +
958A VAL* 6.1 1.1 - - - -
959A ILE 6.3 0.2 - - - +
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Residues in contact with GLN 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A GLY* 4.8 1.8 - - - -
789A PRO* 1.3 80.9 - - + +
791A LEU* 1.3 60.2 + - - +
793A LEU* 3.2 5.7 + - - +
794A ASN* 2.7 62.6 + - - +
950A ALA* 2.9 28.8 + - - +
953A PRO* 3.4 26.9 - - + +
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Residues in contact with LEU 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787A LEU* 4.3 15.0 - - + -
788A GLY* 3.0 19.4 + - - +
790A GLN* 1.3 80.2 - - + +
792A LEU* 1.3 61.7 + - - +
794A ASN* 3.6 14.7 + - + +
795A TRP* 3.3 56.6 + - + -
826A PRO 4.7 2.9 - - - +
827A SER* 4.0 34.5 - - - +
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Residues in contact with LEU 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A VAL* 5.0 4.7 - - + -
787A LEU* 4.4 24.7 - - + -
788A GLY 2.7 19.2 + - - +
789A PRO* 4.2 6.1 - - + +
790A GLN 3.2 0.2 - - - -
791A LEU* 1.3 72.4 - - - +
793A LEU* 1.3 64.9 + - - +
795A TRP* 3.6 21.3 + - + +
796A GLY* 3.7 6.8 + - - -
885A LEU* 4.3 24.7 - - + +
886A MET* 3.3 41.5 - - + +
888A PHE* 4.3 19.7 - - + -
916A ILE* 4.7 5.6 - - + -
957A LEU* 3.8 11.9 - - + -
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Residues in contact with LEU 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789A PRO 3.4 15.5 + - - +
790A GLN 3.2 8.2 + - - +
792A LEU* 1.3 75.6 - - - +
794A ASN* 1.3 64.8 - - - +
795A TRP 3.1 2.0 - - - -
796A GLY* 2.9 15.3 + - - +
797A VAL* 3.2 14.4 + - - +
886A MET* 4.6 2.9 - - + -
921A VAL* 5.2 1.8 - - + -
946A PHE* 3.7 33.0 - - + +
949A MET* 3.8 43.1 - - + +
950A ALA* 4.1 11.9 - - + +
953A PRO* 4.0 21.5 - - + +
956A TYR* 4.9 1.3 - - + -
957A LEU* 3.7 25.1 - - + -
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Residues in contact with ASN 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A GLN* 2.7 53.8 + - - +
791A LEU* 3.6 17.8 - - + +
792A LEU 3.5 0.2 - - - -
793A LEU* 1.3 74.6 - - - +
795A TRP* 1.3 56.7 + - + +
797A VAL* 3.2 11.6 + - - +
798A GLN* 2.8 51.1 + - + +
950A ALA* 4.3 9.8 - - - +
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Residues in contact with TRP 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776A LEU* 3.5 26.5 - - + -
779A HIS* 3.7 26.7 - + - -
780A VAL* 4.6 5.6 - - + -
787A LEU* 4.2 20.0 - - + -
791A LEU* 3.3 42.8 + - + +
792A LEU* 3.8 16.8 - - + +
793A LEU 3.1 0.8 - - - -
794A ASN* 1.3 74.8 - - + +
796A GLY* 1.3 59.5 + - - +
798A GLN* 3.6 12.1 - - - +
799A ILE* 3.0 42.2 + - + +
823A LEU* 3.7 10.8 - - + -
826A PRO 3.6 18.2 - - - -
827A SER 3.1 20.0 + - - -
829A VAL* 3.4 34.4 - - + +
885A LEU* 5.7 6.3 - - + -
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Residues in contact with GLY 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A LEU 3.7 4.2 + - - -
793A LEU 2.9 10.0 + - - -
795A TRP* 1.3 78.4 - - - +
797A VAL* 1.3 61.0 + - - +
799A ILE* 4.8 4.5 - - - -
800A ALA* 3.2 12.1 + - - +
878A TYR* 2.7 31.2 + - - -
882A VAL* 5.0 5.6 - - - -
885A LEU* 6.2 2.0 - - - +
886A MET* 6.2 0.7 - - - -
946A PHE* 4.3 18.4 - - - -
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Residues in contact with VAL 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793A LEU 3.3 15.9 - - - +
794A ASN* 3.4 13.7 - - - +
795A TRP 3.2 0.2 - - - -
796A GLY* 1.3 76.1 - - - +
798A GLN* 1.3 60.4 + - + +
800A ALA* 3.3 6.2 + - - +
801A LYS* 3.0 58.4 + - + +
943A ALA* 4.0 20.0 - - + +
946A PHE* 3.6 23.8 - - + +
947A THR* 3.8 22.2 - - - +
950A ALA* 4.8 4.0 - - + -
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Residues in contact with GLN 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A HIS* 2.9 54.9 - - + +
794A ASN* 2.8 39.9 + - - +
795A TRP* 3.4 4.2 + - - +
797A VAL* 1.3 75.4 - - + +
799A ILE* 1.3 61.9 + - - +
801A LYS* 3.6 4.8 + - + +
802A GLY 3.4 5.5 + - - -
827A SER 3.3 15.4 + - - +
828A GLN* 3.0 29.6 + - - +
829A VAL* 3.1 33.7 + - + +
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Residues in contact with ILE 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751A HIS 5.7 0.2 - - - -
776A LEU* 4.0 13.7 - - + -
795A TRP 3.0 24.8 + - - +
796A GLY* 4.0 6.3 - - - +
798A GLN* 1.3 75.7 - - - +
800A ALA* 1.3 58.0 + - - +
802A GLY* 3.2 3.3 + - - -
803A MET* 3.0 30.9 + - + +
816A LEU* 4.7 6.5 - - + -
821A VAL* 3.8 42.4 - - + -
829A VAL* 4.3 7.0 - - + -
831A VAL* 4.0 19.9 - - + +
878A TYR* 3.6 24.5 - - + -
881A THR* 4.5 6.1 - - + -
882A VAL* 6.0 1.3 - - + -
885A LEU* 4.4 13.0 - - + -
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Residues in contact with ALA 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796A GLY 3.2 15.8 + - - +
797A VAL 3.3 4.7 + - - +
799A ILE* 1.3 80.8 - - - +
801A LYS* 1.3 56.5 - - - +
803A MET* 3.5 0.7 + - - -
804A TYR* 2.9 29.5 + - - +
878A TYR* 3.6 21.3 - - + +
939A PHE* 3.9 18.3 - - + +
942A LEU* 4.3 3.4 - - + -
943A ALA* 3.9 26.9 - - - +
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Residues in contact with LYS 801 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A HIS* 3.8 15.5 + - + -
751A HIS* 4.0 27.9 + - + +
797A VAL* 3.0 41.0 + - + +
798A GLN* 3.7 7.8 - - - +
799A ILE 3.3 0.2 - - - -
800A ALA* 1.3 75.7 - - - +
802A GLY* 1.3 57.8 + - - +
804A TYR* 3.3 12.4 - - - +
805A TYR* 3.0 21.3 + - - +
943A ALA* 4.7 11.2 - - + +
947A THR* 6.0 0.7 - - - -
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Residues in contact with GLY 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A HIS* 4.1 4.5 - - - -
751A HIS* 4.0 15.4 - - - +
752A ILE* 3.9 22.7 - - - +
798A GLN 3.4 4.4 + - - -
799A ILE 3.2 7.1 + - - -
801A LYS* 1.3 76.8 - - - +
803A MET* 1.3 57.4 + - - +
805A TYR* 2.9 20.1 + - - +
806A LEU* 2.9 17.1 + - - +
831A VAL* 4.8 2.2 - - - -
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Residues in contact with MET 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799A ILE* 3.0 25.0 + - + +
800A ALA 3.9 0.4 - - - +
802A GLY* 1.3 74.6 - - - +
804A TYR* 1.3 56.5 + - - +
806A LEU* 3.6 23.8 - - + +
807A GLU* 2.8 28.6 + - - +
811A MET 5.6 1.3 - - - +
813A HIS* 4.0 11.4 - - + +
816A LEU* 3.6 28.7 - - + -
831A VAL* 4.1 15.4 - - + +
874A ASP* 3.7 28.9 - - + +
939A PHE* 3.5 49.2 - - + -
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Residues in contact with TYR 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A HIS* 6.3 0.4 - - - -
800A ALA 2.9 18.9 + - - +
801A LYS* 3.3 11.7 - - - +
802A GLY 3.1 0.2 - - - -
803A MET* 1.3 73.2 - - - +
805A TYR* 1.3 55.5 + - + +
807A GLU* 3.0 13.3 + - + +
808A GLU* 2.8 75.0 + - + +
939A PHE* 4.0 12.9 - - + +
940A LYS* 3.3 55.6 + - + -
943A ALA* 6.1 1.1 - - + -
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Residues in contact with TYR 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746A SER 4.7 1.7 + - - -
747A LEU* 3.6 23.5 - - + -
748A ASP* 2.8 50.3 + - - +
749A HIS* 3.4 41.7 - + + +
752A ILE* 4.0 8.3 - - + -
801A LYS 3.0 8.0 + - - +
802A GLY 2.9 9.3 + - - +
804A TYR* 1.3 77.5 - - + +
806A LEU* 1.3 66.0 + - + +
808A GLU* 3.4 11.8 + - - -
809A HIS* 3.1 61.5 + + - -
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Residues in contact with LEU 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A LEU* 3.5 32.5 - - + -
752A ILE* 4.3 17.7 - - + -
802A GLY 2.9 15.5 + - - +
803A MET* 3.6 33.4 - - + +
805A TYR* 1.3 78.1 - - + +
807A GLU* 1.3 60.3 + - - +
809A HIS 3.4 2.3 + - - -
810A GLY 3.2 3.8 + - - -
811A MET* 2.8 46.8 + - + +
813A HIS* 4.5 7.2 - - + -
831A VAL* 4.6 5.6 - - + -
834A PHE* 3.9 36.3 - - + -
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Residues in contact with GLU 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A MET 2.8 18.7 + - - +
804A TYR* 3.0 15.8 + - + +
806A LEU* 1.3 75.3 - - - +
808A GLU* 1.3 63.1 + - - +
810A GLY* 3.0 11.3 + - - -
811A MET 4.1 0.2 + - - -
871A HIS* 2.9 50.2 + - + +
938A THR* 4.7 9.7 - - - +
939A PHE* 3.6 31.9 + - + +
940A LYS* 5.7 3.8 - - - +
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Residues in contact with GLU 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804A TYR* 2.8 63.5 + - + +
805A TYR* 3.6 16.6 - - - +
807A GLU* 1.3 74.0 - - - +
809A HIS* 1.3 66.5 + - + +
810A GLY 3.4 2.4 + - - -
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Residues in contact with HIS 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A LEU* 3.6 25.1 - - + +
805A TYR* 3.1 62.5 + + - +
806A LEU 3.4 1.3 + - - +
807A GLU 3.3 0.2 - - - -
808A GLU* 1.3 83.4 + - + +
810A GLY* 1.3 60.6 + - - +
811A MET* 3.3 4.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il